HL_5FDV_213

3D structure

PDB id

5FDV (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Pyrrhocoricin antimicrobial peptide bound to the Thermus thermophilus 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

G(PSU)AAC(5MU)A(PSU)AA(OMC)

Length

11 nucleotides

Bulged bases

5FDV|1|2A|A|1913

QA status

Modified nucleotides: PSU, 5MU, OMC

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

HL_5FDV_213 not in the Motif Atlas

Homologous match to HL_9DFE_046

Geometric discrepancy: 0.3723

The information below is about HL_9DFE_046

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

HL_25847.2

Basepair signature

cWW-F-cSH-tHW-F-F-F

Number of instances in this motif group

3

Unit IDs

5FDV|1|2A|G|1910
5FDV|1|2A|PSU|1911
5FDV|1|2A|A|1912
5FDV|1|2A|A|1913
5FDV|1|2A|C|1914
5FDV|1|2A|5MU|1915
5FDV|1|2A|A|1916
5FDV|1|2A|PSU|1917
5FDV|1|2A|A|1918
5FDV|1|2A|A|1919
5FDV|1|2A|OMC|1920

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2a

Small subunit ribosomal RNA; SSU rRNA

Chain 2x

Ribosome-associated inhibitor A